Resolution of Phenotypically Distinct Strains of Enterococcus spp. in a Complex Microbial Community Using cpn60 Universal Target Sequencing
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Characterization of complex microbial communities is frequently based on the examination of polymerase chain reaction amplified sequences from a single phylogenetic marker, usually the 16S rRNA gene. However, this commonly used target often does not offer robust resolution of species or sub-species and is thus not a sufficiently informative target for understanding microbial population dynamics occurring at the strain level. We have used the cpn60 universal target sequence to characterize Enterococcus isolates from feces of growing pigs and have shown that sub-species groups, not detected using 16S rRNA sequences, can be resolved. Furthermore, groups resolved by cpn60-based phylogenetic analysis have distinct phenotypes. We report changes in the structure and function of Enterococcus communities in pig feces sampled from individual animals at three times, from suckling through to maturity. Enterococcus faecalis was largely replaced by Enterococcus hirae between suckling and 9 weeks of age, and a shift from one sub-species group of E. hirae to another was observed in all animals between 9 and 15 weeks. Conversely, E. faecalis strains remained consistent throughout the study period. Our results demonstrate that cpn60 sequences can be used to detect strain level changes in Enterococcus populations during succession in the fecal microbiota of growing pigs.
KeywordsCarbon Source Utilization Canola Meal Natural Microbial Community Fecal Enterococcus Enterococcus Cecorum
The authors gratefully acknowledge John Harding and Crissie Baker for collection of pig fecal samples and Champika Fernando for assistance with statistical analysis. Funding for this work was provided by an NSERC Discovery Grant and a grant from the WCVM Vitamin Fund to JEH. Additional support was provided by NSERC Undergraduate Research Award (AHR) and the University of Saskatchewan (CJV & ARD).
- 11.Dumonceaux TJ, Hill JE, Pelletier C, Paice MG, Van Kessel AG, Hemmingsen SM (2006) Molecular characterization of microbial communities in Canadian pulp and paper activated sludge and quantification of a novel Thiothrix eikelboomii-like bulking filament. Can J Microbiol 52:494CrossRefPubMedGoogle Scholar
- 12.Felsenstein J (1993) PHYLIP (Phylogeny Infererence Package) version 3.5c, distributed by the author. Department of Genetics, University of Washington, SeattleGoogle Scholar
- 14.Goh SH, Facklam RR, Chang M, Hill JE, Tyrrell GJ, Burns EC, Chan D, He C, Rahim T, Shaw C, Hemmingsen SM (2000) Identification of Enterococcus species and phenotypically similar Lactococcus and Vagococcus species by reverse checkerboard hybridization to chaperonin 60 gene sequences. J Clin Microbiol 38:3953PubMedGoogle Scholar
- 17.Hill JE, Paccagnella A, Law K, Melito PL, Woodward DL, Price DL, Ng L-K, Hemmingsen SM, Goh SH (2006) Identification of Campylobacter spp. and discrimination from Helicobacter and Arcobacter spp. by direct sequencing of PCR-amplified cpn60 sequences and comparison to cpnDB, a chaperonin reference sequence database. J Med Microbiol 55:393CrossRefPubMedGoogle Scholar
- 30.Paulsen IT, Banerjei L, Myers GS, Nelson KE, Seshadri R, Read TD, Fouts DE, Eisen JA, Gill SR, Heidelberg JF, Tettelin H, Dodson RJ, Umayam L, Brinkac L, Beanan M, Daugherty S, DeBoy RT, Durkin S, Kolonay J, Madupu R, Nelson W, Vamathevan J, Tran B, Upton J, Hansen T, Shetty J, Khouri H, Utterback T, Radune D, Ketchum KA, Dougherty BA, Fraser CM (2003) Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. Science 299:2071CrossRefPubMedGoogle Scholar
- 31.Perna NT, Plunkett G 3rd, Burland V, Mau B, Glasner JD, Rose DJ, Mayhew GF, Evans PS, Gregor J, Kirkpatrick HA, Posfai G, Hackett J, Klink S, Boutin A, Shao Y, Miller L, Grotbeck EJ, Davis NW, Lim A, Dimalanta ET, Potamousis KD, Apodaca J, Anantharaman TS, Lin J, Yen G, Schwartz DC, Welch RA, Blattner FR (2001) Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409:529CrossRefPubMedGoogle Scholar